Identification of novel methylated targets in colorectal cancer by microarray analysis and construction of co‑expression network

Li,Dongsheng; Guo,Jialin; Wang,Song; Zhu,Liangchen; Shen,Zugang

doi:10.3892/ol.2017.6506

Identification of novel methylated targets in colorectal cancer by microarray analysis and construction of co‑expression network

Authors:
- Dongsheng Li
- Jialin Guo
- Song Wang
- Liangchen Zhu
- Zugang Shen
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Affiliations: Department of General Surgery, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, P.R. China
Published online on: June 30, 2017 https://doi.org/10.3892/ol.2017.6506
Pages: 2643-2648
Copyright: © Li et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

The present study was conducted to investigate novel methylated targets in colorectal cancer (CRC). The mRNA expression profiles of GSE32323 in 17 cancer and non‑cancerous tissues from CRC patients, as well as expression profiles of 5 CRC cell lines prior and subsequent to 5‑aza‑2'‑deoxycytidine (5‑aza‑dC) treatment, were obtained from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) in 5 CRC cell lines prior and subsequent to 5‑aza‑dC treatment were combined with the CRC‑specific gene expression profiling array data. Context likelihood of relatedness algorithm was used to construct the co‑expression network of CRC‑specific gene expression profile. A sub‑network of identified reverse‑overlapped DEGs was selected and underwent Kyoto Encyclopedia of Genes and Genomes Pathway Analysis. A total of 6 reverse‑overlapped DEGs were identified. This present study verified fibulin 2 (FBLN2) and protein phosphatase 1 regulatory inhibitor subunit 14A (PPP1R14A) to be downregulated in the CRC tissue sample but upregulated in CRC cell lines following 5‑aza‑dC treatment. The identified reverse‑overlapped DEGs were enriched in tumor‑associated signaling pathways, including cellular tumor antigen p53, cell cycle and NOD‑like receptor (NLR) signaling pathway. A total of 2 silenced genes with abnormal methylation in CRC were identified, including FBLN2 and PPP1R14A. The reverse‑overlapped DEGs were enriched in p53, cell cycle and NLR signaling pathways, indicating that reverse‑overlapped DEGs, particularly FBLN2 and PPP1R14A, may be important tumor suppressors and that these reverse‑overlapped DEGs are inactivated by methylation in CRC.

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